rs10510211

Variant names:

• chr3-1547846-T-C
• rs10510211

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.248 in 152,136 control chromosomes in the GnomAD database, including 5,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5311 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37784 AN: 152018 Hom.: 5305 Cov.: 34

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.248 AC: 37802 AN: 152136 Hom.: 5311 Cov.: 34 AF XY: 0.242 AC XY: 17976 AN XY: 74380

African (AFR) AF: 0.380 AC: 15747 AN: 41488

American (AMR) AF: 0.175 AC: 2671 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1103 AN: 5168

South Asian (SAS) AF: 0.159 AC: 769 AN: 4832

European-Finnish (FIN) AF: 0.143 AC: 1516 AN: 10602

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14257 AN: 67984

Other (OTH) AF: 0.255 AC: 537 AN: 2110

Alfa AF: 0.212 Hom.: 644

Bravo AF: 0.258

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.30
PhyloP100		-0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10510211; hg19: chr3-1589530;